Learning transport cost from subset correspondence

Learning to align multiple datasets is an important problem with many applications, and it is especially useful when we need to integrate multiple experiments or correct for confounding. Optimal transport (OT) is a principled approach to align datasets, but a key challenge in applying OT is that we need to specify a transport cost function that accurately captures how the two datasets are related. Reliable cost functions are typically not available and practitioners often resort to using hand-crafted or Euclidean cost even if it may not be appropriate. In this work, we investigate how to learn the cost function using a small amount of side information which is often available. The side information we consider captures subset correspondence---i.e. certain subsets of points in the two data sets are known to be related. For example, we may have some images labeled as cars in both datasets; or we may have a common annotated cell type in single-cell data from two batches. We develop an end-to-end optimizer (OT-SI) that differentiates through the Sinkhorn algorithm and effectively learns the suitable cost function from side information. On systematic experiments in images, marriage-matching and single-cell RNA-seq, our method substantially outperform state-of-the-art benchmarks

Learning Cost Functions for Optimal Transport

Inverse optimal transport (OT) refers to the problem of learning the cost function for OT from observed transport plan or its samples. In this paper, we derive an unconstrained convex optimization formulation of the inverse OT problem, which can be further augmented by any customizable regularization. We provide a comprehensive characterization of the properties of inverse OT, including uniqueness of solutions. We also develop two numerical algorithms, one is a fast matrix scaling method based on the Sinkhorn-Knopp algorithm for discrete OT, and the other one is a learning based algorithm that parameterizes the cost function as a deep neural network for continuous OT. The novel framework proposed in the work avoids repeatedly solving a forward OT in each iteration which has been a thorny computational bottleneck for the bi-level optimization in existing inverse OT approaches. Numerical results demonstrate promising efficiency and accuracy advantages of the proposed algorithms over existing state-of-the-art methods

Diffusion Earth Mover's Distance and Distribution Embeddings

We propose a new fast method of measuring distances between large numbers of related high dimensional datasets called the Diffusion Earth Mover's Distance (EMD). We model the datasets as distributions supported on common data graph that is derived from the affinity matrix computed on the combined data. In such cases where the graph is a discretization of an underlying Riemannian closed manifold, we prove that Diffusion EMD is topologically equivalent to the standard EMD with a geodesic ground distance. Diffusion EMD can be computed in $\tilde{O}(n)$ time and is more accurate than similarly fast algorithms such as tree-based EMDs. We also show Diffusion EMD is fully differentiable, making it amenable to future uses in gradient-descent frameworks such as deep neural networks. Finally, we demonstrate an application of Diffusion EMD to single cell data collected from 210 COVID-19 patient samples at Yale New Haven Hospital. Here, Diffusion EMD can derive distances between patients on the manifold of cells at least two orders of magnitude faster than equally accurate methods. This distance matrix between patients can be embedded into a higher level patient manifold which uncovers structure and heterogeneity in patients. More generally, Diffusion EMD is applicable to all datasets that are massively collected in parallel in many medical and biological systems.Comment: Presented at ICML 202